Raman Imaging Metadata Attributes

Fields that are collected for Raman Imaging data, available at dataset.metadata.<attribute>  

* indicates a required field

Attribute Type Description Allowable Values
lab_id A locally assigned identifier provided by the data provider for the dataset. It is used to reference an external metadata record that may be maintained independently, enabling traceability and supporting provenance tracking. Example: Visium_9OLC_A4_S1  
source_storage_duration_value * The length of time the sample was stored prior to processing it. For assays performed on tissue sections, this refers to how long the tissue section (e.g., slide) was stored before the assay began (e.g., imaging). For assays performed on suspensions, such as sequencing, it refers to how long the suspension was stored before library construction started. Example: 12  
time_since_acquisition_instrument_calibration_value The length of time since the acquisition instrument was last serviced or calibrated. This provides a metric for assessing drift in data capture. Example: 10  
contributors_path * The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv  
data_path The top-level directory containing the raw and/or processed data. For a single dataset upload, this might be represented as “.”, whereas for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For example, if the data is within a directory named “TEST001-RK”, use the syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2”, where “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field used solely for data ingestion. Example: ./TEST001-RK  
is_image_preprocessing_required Indicates whether image preprocessing is necessary based on the type of acquisition instrument used, such as a microscope or slide scanner. This may involve steps like fusing image tiles to assemble the complete image. Example: Yes  
slide_id The unique identifier assigned to each slide, enabling users to determine which tissue sections were processed together on the same slide. It is recommended that data providers prefix the ID with the center name to prevent overlapping values across different centers. Example: VAN0071-PA-1-1_AF  
tiled_image_columns The number of columns used in the stitching process of a tiled image, often referred to as the grid size in the x-dimension. Example: 5  
tiled_image_count The total number of raw tiled images captured, which are intended to be stitched together. Example: 75  
intended_tile_overlap_percentage The intended percentage of overlap between tiled images. This value serves as the set point, although slight variations may occur during image acquisition due to stage registration. Example: 5  
dataset_type * The specific type of dataset being produced. Example: RNAseq Visium HD 4i LC-MS Thick section Multiphoton MxIF Light Sheet ATACseq Resolve HiFi-Slide COMET MPLEx 10X Multiome MALDI Raman Imaging Histology Cell DIVE FACS MS Lipidomics Visium (no probes) MUSIC RNAseq GeoMx (NGS) GeoMx (nCounter) RNAseq (with probes) Singular Genomics G4X Molecular Cartography CosMx Transcriptomics MERFISH Pixel-seqV2 2D Imaging Mass Cytometry Confocal seqFISH DART-FISH MIBI Olink Enhanced Stimulated Raman Spectroscopy (SRS) DESI Xenium CyCIF SNARE-seq2 nanoSPLITS STARmap Stereo-seq Visium (with probes) SIMS Auto-fluorescence CyTOF CosMx Proteomics Virtual Histology DBiT-seq PhenoCycler
analyte_class The analyte class which is the target molecule that the assay is measuring. Example: DNA Nucleic acid + protein Lipid + metabolite Collagen RNA Fluorochrome DNA Metabolite DNA + RNA Saturated lipid Lipid RNA + protein Peptide Protein Unsaturated lipid Endogenous fluorophore Chromatin Polysaccharide
acquisition_instrument_vendor The company that manufactures or supplies the acquisition instrument. An acquisition instrument is a device equipped with signal detection hardware and signal processing software. It captures signals produced by assays, such as variations in light intensity or color, or signals corresponding to molecular mass. If the instrument was custom-built or developed internally, enter “In-House”. Example: Illumina Complete Genomics Cytek Biosciences Thermo Fisher Scientific Sciex Vizgen Leica Microsystems Akoya Biosciences Keyence Andor Standard BioTools (Fluidigm) Leica Biosystems Zeiss Microscopy Ionpath Motic In-House Revvity Evident Scientific (Olympus) GE Healthcare Element Biosciences Hamamatsu Waters Bruker Illumina 3DHISTECH Singular Genomics Huron Digital Pathology Resolve Biosciences NanoString Cytiva 10x Genomics Microscopes International BGI Genomics
acquisition_instrument_model The specific model of the acquisition instrument, as manufacturers often offer various versions with differing features or sensitivities. These differences may be relevant to the processing or interpretation of the data. If the instrument was custom-built or developed internally, enter “In-House”. If the model is unknown, enter “Unknown”. Example: HiSeq 4000 NovaSeq X NovaSeq X Plus Cytek Northern Lights Lightsheet 7 Resolve Biosciences Molecular Cartography timsTOF HT timsTOF Pro 2 timsTOF Pro timsTOF Ultra timsTOF Ultra 2 timsTOF SCP Axio Scan.Z1 MALDI timsTOF Flex Prototype CosMx Spatial Molecular Imager Unknown MERSCOPE Ultra Juno System timsTOF FleX Custom: Multiphoton CyTOF XT Helios EVOS M7000 Aperio AT2 Phenocycler-Fusion 2.0 Axio Observer 5 Axio Observer 7 Axio Observer 3 NanoZoomer-SQ NanoZoomer S210 NanoZoomer S60 NanoZoomer S360 DM6 B MoticEasyScan One In-House NextSeq 500 BZ-X710 QTRAP 5500 DMi8 NextSeq 550 HiSeq 2500 HiSeq 4000 NovaSeq 6000 Opera Phenix Plus HCS SYNAPT G2-Si Q Exactive HF Orbitrap Fusion Tribrid Orbitrap Fusion Lumos Tribrid Q Exactive VS200 Slide Scanner Not applicable
source_storage_duration_unit The unit of measurement used to specify the source storage duration value. Example: hour hour month day minute year
time_since_acquisition_instrument_calibration_unit The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month month day year
tile_configuration The configuration of tiles used for stitching in the assay process. If no tile configuration is applicable, enter “Not applicable”. Example: Row-by-row Column-by-column Not applicable Snake-by-columns Row-by-row Snake-by-rows
scan_direction The direction of imaging, which is necessary for the stitching process. Example: Left-and-down Left-and-down Right-and-down Not applicable Right-and-up Left-and-up
metadata_schema_id * The unique string identifier for the metadata specification version, which is easily interpretable by computers for purposes of data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9  
preparation_protocol_doi The DOI for the protocols.io page that details the assay or the procedures used for sample procurement and preparation. For example, in the case of an imaging assay, the protocol may start with tissue section staining and end with the generation of an OME-TIFF file. The documented protocol should also include any image processing steps involved in producing the final OME-TIFF. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1  
is_targeted Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes  
parent_sample_id The unique identifier from HuBMAP or SenNet for the sample (such as a block, section, or suspension) used to perform the assay. For instance, in an RNAseq assay, the parent sample would be the suspension, while in imaging assays, it would be the tissue section. If the assay is derived from multiple parent samples, this field should contain a comma-separated list of identifiers. Example: HBM386.ZGKG.235, HBM672.MKPK.442  
number_of_pixels The total number of spatial sampling points in an image; for example, in a Raman image, each pixel corresponds to one recorded Raman spectrum. Example: 40000  
pixel_physical_size_height_value The physical height of a single pixel in the image. Example: 1000  
pixel_physical_size_height_unit The unit of measurement for the pixel physical size height value. If the pixel height is not specified, this field may be left blank. Example: um um mm nm
pixel_physical_size_width_value The physical width of a single pixel in the image. Example: 1000  
pixel_physical_size_width_unit The unit of measurement for the pixel physical size width value. If the pixel width value is not specified, this field may be left blank. Example: um um mm nm
pixel_physical_size_depth_value The physical depth of a single pixel in the image. Example: 10  
pixel_physical_size_depth_unit The unit of measurement for the pixel physical size depth value. If the pixel depth value is not specified, this field may be left blank. Example: um um mm nm
objective_numerical_aperture Numerical aperture of the microscope objective used to focus the excitation laser on the sample and collect the resulting scattered signal, such as Raman-scattered light. Example: 0.5  
laser_power Power of the excitation laser at the sample’s focal plane, measured after the objective and reported in milliwatts (mW). Example: 10  
raman_shift_range Range of Raman shifts acquired in the measurement, expressed in wavenumbers (cm⁻¹). Example: 400-3200